Crystal structure of Selaginella moellendorffii HCT

Experimental Data Snapshot

  • Resolution: 2.91 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.254 

Starting Model: experimental
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Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT).

Chiang, Y.C.Levsh, O.Lam, C.K.Weng, J.K.Wang, Y.

(2018) PLoS Comput Biol 14: e1006511-e1006511

  • DOI: https://doi.org/10.1371/journal.pcbi.1006511
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Substrate permissiveness has long been regarded as the raw materials for the evolution of new enzymatic functions. In land plants, hydroxycinnamoyltransferase (HCT) is an essential enzyme of the phenylpropanoid metabolism. Although essential enzymes are normally associated with high substrate specificity, HCT can utilize a variety of non-native substrates. To examine the structural and dynamic basis of substrate permissiveness in this enzyme, we report the crystal structure of HCT from Selaginella moellendorffii and molecular dynamics (MD) simulations performed on five orthologous HCTs from several major lineages of land plants. Through altogether 17-μs MD simulations, we demonstrate the prevalent swing motion of an arginine handle on a submicrosecond timescale across all five HCTs, which plays a key role in native substrate recognition by these intrinsically promiscuous enzymes. Our simulations further reveal how a non-native substrate of HCT engages a binding site different from that of the native substrate and diffuses to reach the catalytic center and its co-substrate. By numerically solving the Smoluchowski equation, we show that the presence of such an alternative binding site, even when it is distant from the catalytic center, always increases the reaction rate of a given substrate. However, this increase is only significant for enzyme-substrate reactions heavily influenced by diffusion. In these cases, binding non-native substrates 'off-center' provides an effective rationale to develop substrate permissiveness while maintaining the native functions of promiscuous enzymes.

  • Organizational Affiliation

    Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable hydroxycinnamoyl transferase
A, B
449Selaginella moellendorffiiMutation(s): 0 
Gene Names: BAHDe7-1SELMODRAFT_450171
EC: 2.3.1 (PDB Primary Data), (PDB Primary Data)
Find proteins for D8T7G0 (Selaginella moellendorffii)
Explore D8T7G0 
Go to UniProtKB:  D8T7G0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD8T7G0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.91 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.254 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.39α = 90
b = 83.749β = 90
c = 188.855γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other privateUnited StatesPew Scholar Program in the Biomedical Sciences
Other privateUnited StatesSearle Scholars Program
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103403
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description